Do foreign countries penalize the United States if they find contraband within our cargo?

This question is extremely complicated. The basic answer is, no, foreign countries do not penalize the United States when they find contraband in our cargo. The kind of “contraband” found in US cargo is almost always contraband about which the US government has no knowledge. This is because the United States has a rigorous process for licensing and screening outgoing cargo. Shippers are required to provide documentation attesting to the type and quantity of items being exported and, in certain cases, the destination to which the cargo is being shipped. US government officials from multiple federal agencies, including Customs and Border Patrol, the Drug Enforcement Administration (DEA), and the Department of Commerce, each monitor exports for items that require a special license (e.g., so-called “dual-use” items that have both commercial and military uses) or that are illegal to possess in the first place, such as drugs. The DEA monitors for drugs entering the country hidden in cargo and monitors for the cash (or other items of value) that leaves the country as payment for those drugs.
Besides revenue associated with the illicit trade in narcotics, the main exports from the United States that cause problems abroad involve weaponry and the aforementioned dual-use goods, many of which are used in the development and construction of nuclear and chemical weapons. These are the types of exports that are regulated. When a dual-use item is being shipped to certain countries, like China or Pakistan, the Department of Commerce Bureau of Industry and Security must review and authorize the export—a process in which the Departments of State and Defense play a role, to ensure all potential uses for the items in question are considered. The main problem is that hostile and quasi-hostile governments, like those in Iran, North Korea, Russia, and China, use circuitous routes involving black markets, front companies, and espionage to circumvent the US licensing process. Consequently, what is contraband to the United States is not contraband to those other countries. They do not penalize the United States; it is the United States that penalizes them when these illicit procurement systems are discovered.
The only “contraband” leaving the United States which results in penalization of the United States involves ideas. During the Cold War, the Soviet Union devoted a great deal of time and effort to preventing the import of anything associated with political and religious freedom, such as Bibles and political tracts. Similarly, China today continues to guard against the introduction of American ideals that could threaten Communist Party control. China in particular will penalize the United States when it believes the US government has condoned or authorized the export to China of technologies or ideas that complicate the Chinese government’s determination to regulate the flow of information. China will, then, retaliate by sanctioning US activities in China, including banning American companies from doing business in that huge market, and it will disrupt official US operations there.
In short, contraband leaving the United States is very rarely an issue. Cash associated with drug trafficking, and material threatening to hostile regimes’ hold on power, constitutes the bulk of such exports. Militarily sensitive goods are regulated and only leave the country destined for certain regimes when efforts are made by importers across the ocean to violate US export laws and evade American border controls.